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<h1>Cleaning Options in Marvin</h1>

<p>Both 2D and 3D options can be divided into two groups: <i>Base</i>
and <i>Extra</i>.
<i>Base</i> contains the typically used options which are also
accessible via "Edit/Clean" menu in Marvin. You can use them in each
case.
<i>Extra</i> includes further options which are accepted only by the
MolConvert application and the clean method of MoleculeGraph in the
Marvin Beans API.</p>
<h2><a class="anchor" name="2d">2D options</a></h2>
<ul>
  <li><a class="text" name="base.2d"><b>Base:</b> (none available)</a>
  <li><a class="text" name="extra.2d"><b>Extra:</b></a>
    <p> <i>e</i> Keep verbose either flag<br>
    </p>
    <ul>
If it is not possible to decide whether
the double bond is CIS or TRANS, the double
bond either flag (crossed double bond) is kept.<br>
Otherwise, the flag is removed and converted to double bond
with a wiggly bond.
    </ul>
    <p> <i>E</i> Error output:</p>
    <ul>
	0 - no output (default)<br>
	1 - error output to standard error 
    </ul>

    <p> <i>d</i> show debugging info</p>
    <p> <i>2</i> try to keep actual 2D alignment</p>
    <p> <i>p</i> ignore parity setting </p>
    <ul>
    do not set wedges, the parity information is lost.
    </ul>
    <p> <i>H</i> add Hydrogens</p>
    <ul> Add Hydrogen atoms to chiral centers<br> 
         having no terminal atoms.
    </ul>
    <p> <i>w</i> wedge clean</p>
    <ul> Do not try to keep the actual wedge arrangement,<br>
        but rearrange the wedges also.
    </ul>
    <p> <i>W</i> stereo clean</p>
    <ul> Only rearrange the wedges of the molecule, 
        but keep the original coordinates untouched.
    </ul>
    <p> <i>tX</i> set time limit to X ms </p>
    <ul>maximum time spent in the cleaning<br>
    default value: 20000ms<br>
    if X&lt;1, no time limit used
    </ul>
    <p> <i>T{filename}</i> ring system template file name<br>
    </p>
    <ul>
Use the template file during ring system cleaning together with
the local template file definition
(which is located at the users home directory .chemaxon/cleantemplates.t).
    </ul>
  </li>
</ul>
<h2><a class="anchor" name="3d">3D options</a></h2>
<ul>
  <li><a class="text" name="base.3d"><b>Base:</b></a>
    <p> <i>S{fine}</i> Find low energy conformer. Leave failed
fragments intact. </p>
    <p> <i>S{fast}</i> Fast clean, if failed, perform fine clean,
accept any generated structure (default)</p>
    <p><small>Notes: <i>null</i> always specifies the default value. <i>O0</i>
and <i>OD</i> are deprecated. They use the default value.</small></p>
  </li>
  <li><a class="text" name="extra.3d"><b>Extra:</b></a>
    <p> <i>?</i> Print the complete list of options to <code>System.err</code>.
The same list can be printed by invoking the <a
 href="../applications/molconvert.html">MolConverter</a>
with <span style="font-style: italic;">the -H3D </span>option. <br>
    </p>
    <p> <i>S{nofaulty}</i> Same as <span style="font-style: italic;">S{fast}</span>,
but leave failed fragments intact. </p>
    <p> <i>S{conformers}</i> Generate conformers, store the calculated
conformer coordinates and energies in PropertyObjects. </p>
    <p> <i>E</i> Store calculated Dreiding energy in SDF property
string. The Dreiding energy for each fragment will be calculated in the
last step.&nbsp; Their sum will be stored in the sdf property called
"Energy".<br>
    </p>
  </li>
</ul>
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